Compositions and methods to barcode bacteriophage receptors, and uses thereof

Abstract

The present invention provides for a nucleic acid encoding a bacteriophage genome comprising a unique n-mer barcode inserted in a non-essential location or gene location within the bacteriophage genome, or a bacteriophage comprising the nucleic acid thereof

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application claims priority to U.S. Provisional Patent Application Ser. No. 62 / 971,130, filed on Feb. 6, 2020, which is hereby incorporated by reference in its entirety.STATEMENT OF GOVERNMENTAL SUPPORT[0002]The invention was made with government support under Contract Nos. DE-AC02-05CH11231 awarded by the U.S. Department of Energy. The government has certain rights in the invention.FIELD OF THE INVENTION[0003]The present invention is in the field of engineered bacteriophages.BACKGROUND OF THE INVENTION[0004]Increasing incidents of multidrug resistant bacteria and decrease in the development of new antibiotics have resulted in a global public health concern prompting scientists to seek alternative therapies (Ventola, 2015). Bacteriophages (phages), which infect specific bacterial strains, have been suggested as potential agents to combat this growing threat of multidrug resistant bacterial pathogenesis. Currently, phages are approved...

AI Technical Summary

Benefits of technology

The patent describes a new technology called bacteriophage barcoded DNA (n-mer DNA barcode) that allows for the easy identification, quantification, and tracking of bacteriophages. The n-mer DNA barcode is a unique sequence of DNA that is inserted into a non-essential gene location and is flanked by known primers. The n-mer bar code is not harmful to the host bacterium and can be easily amplified and identified using high-throughput DNA barcode sequencing readouts. This technology also allows for the creation of a handle for identifying, quantifying, and tracking barcoded phages, protecting the effort and investment of isolating the biological agent.

Problems solved by technology

Despite improvements in sequencing technologies, there are many technological gaps that need an urgent attention before we realize the full potential of phage therapy.

One of the key challenges that needs attention is to develop methods to quantify and track phages if we hope to make phage therapy a reality.

The current methods can be applied to sequence phage genomes in the field applications, but will need substantial investment of money, time and labor to extend it to thousands of samples in diverse environments to track and quantify phages or phage cocktails.

Such ‘formulation modifications’ are common in field applications, but there is no standard way to track these changes, quantify the performance of the formulation or individual phages in an economical way.

For example, if a particular phage formulation is used in the meat processing plant, there is no way to quantify and track about how the phage formulation is performing.

These challenges become seriously limited when we envision in scaling up or cataloguing thousands of different phages available in phage directories.

Recently, qPCR platform has been developed to quantify phages in a cocktail, but this technique is still low-throughput (Duyvejonck et al., 2019).

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